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Expression profile analysis of long non-coding RNA in skeletal muscle of osteoporosis by microarray and bioinformatics

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JOURNAL OF BIOLOGICAL ENGINEERING 2019年第1期13卷 50-50页

作者： Liu, Shaojin Huang, Hongxing Chai, Shuang Wei, Hewei Huang, Jiachun Wan, Lei Guangzhou Univ Chinese Med Guangzhou 510405 Guangdong Peoples R China Guangzhou Univ Chinese Med Affiliated Hosp 3 Dept Orthopaed Guangzhou 510378 Guangdong Peoples R China Guangzhou Univ Chinese Med Lingnan Med Res Ctr Guangzhou 510405 Guangdong Peoples R China

Background: Osteoporosis (OP) is a condition featured by bone mass loss and bone tissue microarchitectural alterations due to impaired tissue homeostasis favoring excessive bone resorption versus deposition. The trigger of such an impairment and the downstream molecular pathways involved are yet to be clarified. Long non-coding RNA (lncRNA) plays a role in gene transcription, protein expression and epigenetic regulation;and altered expression results in immune or metabolism related desease development. To determine whether lncRNAs are involved in osteoporosis, we analyzed the expression profile of lncRNAs and mRNAs in osteoporosis. Method: Three pairs of osteoporosis patients (OP group) and healthy people controls (NC group) were screened by microarray. Quantitative polymerase chain reaction (qRT-PCR) was performed to confirm dysregulated lncRNA expressions in 5 pairs of OP and NC group tissues samples. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to construct the lncRNA-mRNA co-expression network. Result: Through co-expression analysis, differently expressed transcripts were divided into modules, and lncRNAs were functionally annotated. We further analyzed the clinical significance of crucial lncRNAs from modules in public data. Finally, the expression of five lncRNAs, CUST_44695_PI430048170-GeneSymbol:CTA-384D8.35;CUST_39447_PI430048170,CUST_73298_PI430048170,CUST_108340_PI430048170,CUST_118927_PI430048170,this four lncRNAs have not been annotation genes and have not found GeneSymbols, and by quantitative RT-PCR, which may be associated with osteoporosis patients' overall survival. Conclusion: Analysis of this study revealed that dysregulated lncRNAs and mRNAs in osteoporosis patients and health people controls could affect the immune or metabolism system and musculoskeletal cell differentiation. The biological functions of those lncRNAs need to be further validated.

关键词： lncRNA microarray profile Musculoskeletal Osteoporosis Quantitative real-time PCR

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Expression changes in protein-coding genes and long non-coding RNAs in denatured dermis following thermal injury

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BURNS 2020年第5期46卷 1128-1135页

作者： Yu, Wenchang Guo, Zaiwen Liang, Pengfei Jiang, Bimei Guo, Le Duan, Mengting Huang, Xu Zhang, Pihong Zhang, Minghua Ren, Licheng Zeng, Jizhang Huang, Xiaoyuan Cent South Univ Xiangya Hosp Dept Burns & Plast Surg Changsha 410008 Hunan Peoples R China Nanjing Med Univ Dept Burn & Plast Surg Suzhou Hosp Suzhou 215002 Jiangsu Peoples R China Cent South Univ Xiangya Sch Med Dept Pathophysiol Changsha 410008 Hunan Peoples R China Cent South Univ Xiangya Hosp Dept Hyperbar Oxygen Changsha 410008 Hunan Peoples R China

Objective: Thermal injury repair is a complex process during which maintaining the proliferation of human dermis fibroblasts (HDFs) and synthesis of extracellular matrix (ECM) plays a critical role. In the present study, we analyzed potential molecular markers and the probable association between differentially-expressed lncRNAs and protein-coding genes within denatured dermis following thermal injury, attempting to provide further insights to thermal injury repair pathogenesis. Methods and main results: We found that the expression of 3940 lncRNAs was increased, while that of 1438 lncRNAs was reduced in the denatured dermis following thermal injury when compared to normal tissue. Of them, 338 were upregulated and 154 were downregulated by more than 128 times. Via cross-check with another microarray profile analysis on differentially-expressed lncRNAs after thermal injury, LINC00302 was found to be downregulated after thermal injury;more importantly, this skin-specially expressed lncRNA is located near a series of genes related to multiple skin inflammation and skin barrier-associated genomes. LINC00302 overexpression promoted the cell viability and the protein levels of alpha-SMA and Collagen I in HDFs. Conclusions: In conclusion, mRNAs and lncRNAs could be differentially expressed in the denatured dermis following thermal injury. mRNA and lncRNA regulatory signaling pathways could participate in thermal injury repair pathogenesis. More importantly, LINC00302 may play a critical role in thermal injury repair. (C) 2019 Elsevier Ltd and ISBI. All rights reserved.

关键词： Denatured dermis Thermal injury microarray profile mRNA lncRNA LINC00302

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Kruppel Like Factors Family Expression in Cervical Cancer Cells

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ARCHIVES OF MEDICAL RESEARCH 2017年第4期48卷 314-322页

作者： Marrero-Rodriguez, Daniel Arreola-De la Cruz, Hugo Taniguchi-Ponciano, Keiko Gomez-Virgilio, Laura Huerta-Padilla, Victor Ponce-Navarrete, Gustavo Andonegui-Elguera, Sergio Jimenez-Vega, Florinda Romero-Morelos, Pablo Rodriguez-Esquivel, Miriam Meraz-Rios, Marco del Pilar Figueroa-Corona, Ma Monroy, Alberto Perez-Gonzalez, Oscar Salcedo, Mauricio Hosp Oncol Inst Mexicano Seguro Social CMN SXXI Lab Oncol GenomUnidad Invest Med Enfermedades On Av Cuauhtemoc 330 Mexico City 06720 DF Mexico Ctr Invest & Estudios Avanzados Dept Biomed Mol Mexico City DF Mexico Univ Autonoma Ciudad Juarez Lab Biotecnol Chihuahua Mexico Inst Mexicano Seguro Social Hosp Oncol CMN SXXI Lab Inmmunol & CancUnidad Invest Med Enfermedade Mexico City DF Mexico Inst Nacl Pediat Lab Oncol Expt SS Mexico City DF Mexico

Background and Aims. Kruppel Like Factors (KLF) refers to a family of seventeen members of transcription factors. Involved in several cellular processes. As other cancer types, Cervical Cancer (CC) presents molecular deregulations in transcription factors, but especially Human Papilloma Virus (HPV) sequences. Here in this work we analyzed the mRNA expression of all KLF family members in CC-derived cell lines and CC tissues. Methods. The cell lines used were HeLa, INBL, RoVa, C4-I, Ms751, ViPa, CaLo, SiHa, CaSki, C33a and ViBo and the non-tumorigenic HaCaT. mRNA expression was analyzed by means of expression microarray and RT-PCR, and KLF5 protein by immunofluorescence. Results. The cell lines were grouped according to HPV genotype as HPV16, HPV18 positive or HPV negative cells. Heterogeneous expression was observed among the cell lines. Despite the heterogeneous expression profile, KLF3, -5, -12, -15 and -16 transcripts were present in all cell lines, KLF4 and -10 which were not expressed in CaSki;KLF11 and 13 were not expressed by Vipa and C4-I, and KLF7 was not expressed by C4-I and Rova. The CC tissue analysis shows expression of most of the KLF members, such as KLF5. KLF5 immunosignal was positive in the three cell lines analyzed. Conclusions. We suggest that KLF expression could not be related to HPV presence/genotype, at least at transcriptional level, and the expression of KLF family members may be necessary in the biology of the CC cells. (C) 2017 IMSS. Published by Elsevier Inc.

关键词： Kruppel Like Factors Cervical cancer Cell lines microarray profile Expression Protein

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Epi-letters - how to describe epigenetic signatures

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BMC Bioinformatics 2012年第SUPPL 18期13卷 A4-A4页

作者： Huy Q Dinh Center for Integrative Bioinformatics Vienna Max F. Perutz Laboratories University of Vienna Medical University of Vienna A-1030 Vienna Austria Gregor Mendel Institute of Molecular Plant Biology Austrian Academy of Sciences A-1030 Vienna Austria

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Variation of gene expression profile linked to p27 ^Kip1 Ser¹⁰ phosphorylation status in MCF-7 cell line

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BIOMEDICINE & PHARMACOTHERAPY 2011年第8期65卷 537-541页

作者： Guan, Xiaoxiang Du, Lili Chen, Longbang Chen, Yitian Wang, Jinghua Nanjing Univ Dept Oncol Jinling Hosp Sch Med Nanjing 210002 Peoples R China

Ser(10) was the major phosphorylation site in p27(Kip1) (here after referred to as p27), accounting for 70% of the total phosphorylation of this protein, due to cytoplasmic shuttling. To further elucidate the mechanism for Ser(10)-mediated dysfunction of p27 during breast cancer progression. Affymetrix Human Genome U133A Array was used to identify differentially regulated genes between MCF-7 breast cancer cell lines stably-transfected with wild type and Ser(10) mutant (substitution of Ser(10) with Ala, S10A), alternatively. Then to confirm by RT-PCR then western blot partly. microarray analysis showing that S10A, then abrogation of Ser(10) phosphorylation, result in important changes in a large number of genes involved in the control of cell cycle, cell differentiation, metabolism, immune response and signal transduction. S10A induced cell cycle G(0) phase arrest by FACS method. And cell growth inhibition and abrogation of cytoplasmic translation. Our data indicate that abrogation of phosphorylation of Ser(10) resulted in significant changes in gene expression profiles which mediate cell cycle redistribution, subcellular localization. Crown Copyright (C) 2010 Published by Elsevier Masson SAS. All rights reserved.

关键词： p27(Kip1) microarray profile Phosphorylation Breast cancer MCF-7 cell line

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microarray data integration for genome-wide analysis of human tissue-selective gene expression

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BMC GENOMICS 2010年第2-Sup期11卷 S15-S15页

作者： Wang, Liangjiang Srivastava, Anand K. Schwartz, Charles E. Clemson Univ Dept Genet & Biochem Clemson SC 29634 USA Greenwood Genet Ctr JC Self Res Inst Human Genet Greenwood SC 29646 USA

Background: microarray gene expression data are accumulating in public databases. The expression profiles contain valuable information for understanding human gene expression patterns. However, the effective use of public microarray data requires integrating the expression profiles from heterogeneous sources. Results: In this study, we have compiled a compendium of microarray expression profiles of various human tissue samples. The microarray raw data generated in different research laboratories have been obtained and combined into a single dataset after data normalization and transformation. To demonstrate the usefulness of the integrated microarray data for studying human gene expression patterns, we have analyzed the dataset to identify potential tissue-selective genes. A new method has been proposed for genome-wide identification of tissue-selective gene targets using both microarray intensity values and detection calls. The candidate genes for brain, liver and testis-selective expression have been examined, and the results suggest that our approach can select some interesting gene targets for further experimental studies. Conclusion: A computational approach has been developed in this study for combining microarray expression profiles from heterogeneous sources. The integrated microarray data can be used to investigate tissue-selective expression patterns of human genes.

关键词： microarray profile Priority Score Detection Call microarray Expression profile Control Array

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Multi-targeted priming for genome-wide gene expression assays

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BMC GENOMICS 2010年第1期11卷 477-477页

作者： Adomas, Aleksandra B. Lopez-Giraldez, Francesc Clark, Travis A. Wang, Zheng Townsend, Jeffrey P. Yale Univ Dept Ecol & Evolutionary Biol Program Computat Biol & Bioinformat New Haven CT 06511 USA Yale Univ Microbiol Grad Program New Haven CT 06511 USA

Background: Complementary approaches to assaying global gene expression are needed to assess gene expression in regions that are poorly assayed by current methodologies. A key component of nearly all gene expression assays is the reverse transcription of transcribed sequences that has traditionally been performed by priming the poly-A tails on many of the transcribed genes in eukaryotes with oligo-dT, or by priming RNA indiscriminately with random hexamers. We designed an algorithm to find common sequence motifs that were present within most protein-coding genes of Saccharomyces cerevisiae and of Neurospora crassa, but that were not present within their ribosomal RNA or transfer RNA genes. We then experimentally tested whether degenerately priming these motifs with multi-targeted primers improved the accuracy and completeness of transcriptomic assays. Results: We discovered two multi-targeted primers that would prime a preponderance of genes in the genomes of Saccharomyces cerevisiae and Neurospora crassa while avoiding priming ribosomal RNA or transfer RNA. Examining the response of Saccharomyces cerevisiae to nitrogen deficiency and profiling Neurospora crassa early sexual development, we demonstrated that using multi-targeted primers in reverse transcription led to superior performance of microarray profiling and next-generation RNA tag sequencing. Priming with multi-targeted primers in addition to oligo-dT resulted in higher sensitivity, a larger number of well-measured genes and greater power to detect differences in gene expression. Conclusions: Our results provide the most complete and detailed expression profiles of the yeast nitrogen starvation response and N. crassa early sexual development to date. Furthermore, our multi-targeting priming methodology for genome-wide gene expression assays provides selective targeting of multiple sequences and counter-selection against undesirable sequences, facilitating a more complete and precise assay of the transcribed

关键词： Sexual Development Nitrogen Starvation Digital Gene Expression Nitrogen Deficiency microarray profile

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Transcriptome bioinformatic analysis identifies potential therapeutic mechanism of pentylenetetrazole in down syndrome

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BIODATA MINING 2010年第1期3卷 7-7页

作者： Sharma, Abhay CSIR Inst Genom & Integrat Biol Delhi 110007 India

Background: Pentylenetetrazole (PTZ) has recently been found to ameliorate cognitive impairment in rodent models of Down syndrome (DS). The mechanism underlying PTZ's therapeutic effect in DS is however not clear. microarray profiling has previously reported differential expression, both up- and down-regulation, of genes in DS. Given this, transcriptomic data related to PTZ treatment, if available, could be used to understand the drug's therapeutic mechanism in DS. No such mammalian data however exists. Nevertheless, a Drosophila model inspired by PTZ induced kindling plasticity in rodents has recently been described. microarray profiling has shown PTZ's downregulatory effect on gene expression in the fly heads. Methods: In a comparative transcriptomics approach, I have analyzed the available microarray data in order to identify potential therapeutic mechanism of PTZ in DS. In the analysis, summary data of up- and down-regulated genes reported in human DS studies and of down-regulated genes reported in the Drosophila model has been used. Results: I find that transcriptomic correlate of chronic PTZ in Drosophila counteracts that of DS. Genes downregulated by PTZ significantly over-represent genes upregulated in DS and under-represent genes downregulated in DS. Further, the genes which are common in the downregulated and upregulated DS set show enrichment for MAP kinase pathway. Conclusion: My analysis suggests that downregulation of MAP kinase pathway may mediate therapeutic effect of PTZ in DS. Existing evidence implicating MAP kinase pathway in DS supports this observation.

关键词： Down Syndrome microarray profile Pentylenetetrazole Drosophila Model Natural Killer Cell Mediate Cytotoxicity

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The footprints of cancer development: Cancer biomarkers

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CANCER TREATMENT REVIEWS 2009年第3期35卷 193-200页

作者： Ullah, Mohd. Fahad Aatif, Mohammad Aligarh Muslim Univ Fac Life Sci Dept Biochem Aligarh 202002 Uttar Pradesh India

Diagnostic detection and measurement of cancer disease progression are essential elements for successful cancer disease management. The early stages of cancer development carry the maximum potential for therapeutic interventions. However, these stages are often asymptomatic, leading to delayed diagnosis at the very advanced stages when effective treatments are unavailing. The application of biomarkers to cancer is leading the way because of the unique association of genomic changes in cancer cells with the disease process. They have the potential to not only help identify who will develop cancer but also to predict as to when the event is most likely to occur. In recent years, there has been an enormous effort to develop specific and sensitive biomarkers for precise and accurate screening, diagnosis, prognosis and monitoring of high risk cancer to assist with therapeutic decisions. The present article is a brief review of the emerging trends in the development of biomarkers for early detection and precise evaluation of cancer disease. (C) 2008 Elsevier Ltd. All rights reserved.

关键词： Biomarkers Diagnosis Proteomics Cancer microarray profile

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Complementary RNA amplification methods enhance microarray identification of transcripts expressed in the C. elegans nervous system

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BMC GENOMICS 2008年第1期9卷 84-84页

作者： Watson, Joseph D. Wang, Shenglong Von Stetina, Stephen E. Spencer, Clay Levy, Shawn Dexheimer, Phillip J. Kurn, Nurith Heath, Joe Don Miller, David M., III Vanderbilt Univ Dept Cell & Dev Biol Nashville TN 37232 USA Vanderbilt Univ Ctr Mol Neurosci Grad Program Neurosci Nashville TN 37232 USA NuGEN Technol Inc San Carlos CA 94070 USA Vanderbilt Univ Dept Biomed Informat Nashville TN 37232 USA

Background: DNA microarrays provide a powerful method for global analysis of gene expression. The application of this technology to specific cell types and tissues, however, is typically limited by small amounts of available mRNA, thereby necessitating amplification. Here we compare microarray results obtained with two different methods of RNA amplification to profile gene expression in the C. elegans larval nervous system. Results: We used the mRNA-tagging strategy to isolate transcripts specifically from C. elegans larval neurons. The WT-Ovation Pico System (WT-Pico) was used to amplify 2 ng of pan-neural RNA to produce labeled cDNA for microarray analysis. These WT-Pico-derived data were compared to microarray results obtained with a labeled aRNA target generated by two rounds of In Vitro Transcription (IVT) of 25 ng of pan-neural RNA. WT-Pico results in a higher fraction of present calls than IVT, a finding consistent with the proposal that DNA-DNA hybridization results in lower mismatch signals than the RNA-DNA heteroduplexes produced by IVT amplification. microarray data sets from these samples were compared to a reference profile of all larval cells to identify transcripts with elevated expression in neurons. These results were validated by the high proportion of known neuron-expressed genes detected in these profiles and by promoter-GFP constructs for previously uncharacterized genes in these data sets. Together, the IVT and WT-Pico methods identified 2,173 unique neuron-enriched transcripts. Only about half of these transcripts (1,044), however, are detected as enriched by both IVT and WT-Pico amplification. Conclusion: We show that two different methods of RNA amplification, IVT and WT-Pico, produce valid microarray profiles of gene expression in the C. elegans larval nervous system with a low rate of false positives. However, our results also show that each method of RNA amplification detects a unique subset of bona fide neural-enriched transcripts and th

关键词： Amplification Method microarray profile Present Call Larval Nervous System Enrich Transcript

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